Of the viruses belonging to the family Orthomyxoviridae, influenza A virus is the most predominant cause of morbidity
and mortality in humans, in which it causes respiratory illness. The natural hosts of all influenza A subtypes are wild
birds, primarily those belonging to the family Anatidae (ducks, geese, and swans). Transmission of numerous subtypes to
humans and other animals have been documented, but establishment of persistent infection of new subtypes in humans is
rare. Apart from waterfowl and humans, transmission of influenza A is known to persist in birds of the order
Galliformes, pigs, horses, and dogs.

Influenza A viruses are classified into subtypes based on the antigenic relationships of their two major surface
proteins: haemagglutinin (HA), which binds to sialic acid residues on surface proteins of host cells, and induces
fusion of the virus membrane with that of the host cell; and neuraminidase (NA), which cleaves sialic acid residues
from surface proteins, enabling release of virus particles from host cells.

Until recently, two influenza A subtypes - H1N1 and H3N2 - persisted in humans, and caused seasonal epidemics of
influenza in temperate countries, and year-round infections in humans in tropical regions. In 2009, a new variant of
H1N1, distantly related to seasonal H1N1, emerged in the human population, and caused the first influenza pandemic of
the 21st century - this virus is now referred to as pandemic (H1N1) 2009.

Data Downloads

This project is ongoing and data for this organism will be made available in due course.

The Wellcome Trust Sanger Institute is committed to two facets of influenza A virus sequencing: whole genome
sequencing; and deep amplicon sequencing.

Our influenza whole genome sequencing is funded by the Wellcome Trust, and involves collaboration with researchers at the Health Protection
Agency (HPA), National Institute for Medical Research, London (NIMR), and the Veterinary Laboratories Agency (VLA).
We have developed robust approaches to sequencing influenza A genomes using capillary, 454, and Illumina sequencing
platforms. The role of these projects is to supplement the sequences of subgenomic genes/segments, which are rapidly
generated by our collaborators, with whole genome consensus sequences.

Our deep amplicon sequencing projects are also funded by the Wellcome Trust, and involve collaborations with the Cambridge Infectious Disease
Consortium (CIDC) and the Animal Health Trust, Newmarket (AHT). Rather than generating consensus sequence for the
whole genome, these projects involve deep sequencing of some genes (usually HA1), to investigate changes in frequency
of rare variants over time during infection, both within the period of infection of an individual and through chains
of transmission.

Related links

Data Use Statement

This sequencing centre plans on publishing the completed and annotated sequences in a
peer-reviewed journal as soon as possible. Permission of the principal investigator should be
obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or
genome scale. See our data sharing policy.